IIS University - International College for Girls - ICG Courses

M.Sc. (Bioinformatics)

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Duration: 2 Years

Eligibility: Graduation and Equivalent

Course Structure

Course Code	Course Title
Semester  -I
BIF  121	* Optional Basic Biology Basic Mathematics
BIF  122	Introduction to Bioinformatics
BIF  123	Computer Fundamentals and Programming in C
BIF  124	Networking and Internet Programming
BIF  125	Biochemistry
BIF  126	Bioinformatics Lab. I (Based on BIF 122)
BIF  127	Computer Lab. I (Based on BIF 123 & 124)
Semester - II
BIF  221	Molecular Biology
BIF  222	Structural Bioinformatics
BIF  223	Data Structures and Algorithms
BIF  224	Object Oriented Programming Language
BIF  225	Molecular Genetics andGenomics
BIF  226	Bioinformatics Lab. II (Based on BIF 222 &225)
BIF  227	Computer Lab. II (Based on BIF 223 &224)
Semester - III
BIF 321	Bioinformatics Algorithms and Perl Programming
BIF 322	Statistics
BIF 323	Biophysical Techniques
BIF 324	Database Management System
BIF 325	** Optional Computer Aided Drug Designing Soft Computing and Machine  Learning Techniques Computer Graphics Genomics and Proteomics
BIF 326	Bioinformatics Lab. III (Based on BIF 321)
BIF 327	Computer Lab. III (Based on BIF 324 & 325 (A-D)
BIF 328	Seminar
Semester - IV
BIF 421	Project Work
BIF 422	Review

Course Syllabus

Semester - I

BIF 121 A  Basic Biology

Unit I Cell: The unit of life

Cell as a basic unit of living system. Structure of Prokaryotic(Bacteria) and Eukaryotic cells(Animal cell and Plant cell).Structure and function of cell organelles-Plasma membrane, cell wall, nucleus, Golgi Bodies, Endoplasmic reticulum (rough and smooth), Ribosome, Mitochondria, Chloroplast, Lysosomes and Microbodies.

Unit II Cell motility and interactions:

Cytoskeleton:Self-assembly and dynamic structure of cytosketetal filaments, actin filament, microtubules, movement of cilia and flagella.

Cell –Cell interaction: cell adhesion, tight and gap junctions, plasmodesmata.

Unit III Bacteria and Viruses

Systematics: Species concept.

Bacteria: Bacterial shapes and arrangement, cell membrane, cell wall of bacteria, inclusion bodies, flagella, capsule, slime, fimbriae, and pilli.Bacterial endosporesstructure. Phylogeny. Characteristics of primary domains.

Viruses : Biology of viruses; bacteriophages, plant and animal viruses; replication of viral genome.

Unit IV Plant Diversity and classification

Algae, Fungi and Higher Plants. Broad classification of Plant Kingdom up to classes.

Unit V Animal Life and classification 8hrs

Major animal phyla and their characteristics. (up to classes).

 

 

BIF 121 B  Basic Mathematics

Unit I Calculus

Limits, Complete Differentials, Partial differentials of functions with one variable and multiple variables.

Unit II Integration & Differential Equation 14hrs

Elementary Integration, Definite and Non-definite integral; Series, Logarithms. Ordinary differential equations (first order), Partial differential equations.

Unit III Vector

Addition, subtraction, dot, cross, scalar triple product, divergence, curl of a vector, equation of normal

Unit IV Matrix algebra

Addition, subtraction, multiplication, transpose inverse, and conjugate of matrix etc.

Unit V Trigonometric functions 10hrs

Sin, Cos, Tan, Cot, Series expansion of these functions and other related functions

 

 

BIF 122  Introduction to Bioinformatics

Unit I Introduction

Definition, History and Application areas of Bioinformatics. Major Information Resources: NCBI, EBI, ExPasy, TIGR, JGI, DDBJ Biological Databases: Primary & Secondary; Structure Databases, Specialized Databases, Chemical Databases, Entrez and SRS, Sequin & Bankit.

Unit II File Formats in Bioinformatics

Genbank, EMBL, Swissprot/Uniprot, PDB, Clustal, MSF, GCG, FASTA etc.

Unit III Sequence Similarity Searching

Basics of sequence alignment, Local and Global Sequence Alignment, similarity, Identity, homology, Sensitivity/Selectivity, Scoring System & Substitution Matrices: Distance and Similarity matrices, Identity Matrices, PAM & BLOSUM matrices & their Derivation

Unit IV Similarity Searching Tools

BLAST and FASTA, Theory and Algorithms, variants of BLAST and FASTA, PSI & PHI Blast, Statistical Significance.

Sequence Pattern and Profiles: Concepts of motif, pattern and profile. Profile construction and its application in Bioinformatics.

Unit V Tools for DNA & Protein Sequence Analysis

EMBOSS, PHYLIP, Mega2, CLustalX/W etc. Tools at NCBI, EBI, DDBJ, ExPasy

 

 

BIF 123  Computer Fundamentals and Programming in C

Unit I Introduction to computers

Characteristics & capabilities; classification; Components of computer system with Block Diagram, CPU, only preliminary concept of Software, Hardware, Low Level Language, High Level Language, Compiler and Interpreter.

Operating Systems: Introduction to operating Systems: WINDOWS, UNIX, Linux operating systems.

Unit II C Programming basics & control structures

Basics of C programming, Structure of a simple C program, Simple I/o functions, Data types in C, operators & their precedence, Control Structures: if-else statements, switch statement, loops: while, do-while and for loop.

Unit III Functions

User-defined functions, returning a value from a function, local & Global variables, automatic, Static Register and External Storage class.

Parameters: Type, declaration of a function, functions with more than one parameters, recursion, Arrays: arrays (up to 2 dimensions), Declaration and initialization, the break structured, string and character arrays, operations with arrays, The C preprocessors. String and string functions.

Structures: Initializing a structure, Arrays of structures, arrays within structures, structures within structures; Structures and functions, Unions

Unit IV Pointers in C

Pointers, the concept of pointers, the address and indirection operators, passing pointers as parameters. Dynamic memory allocation, Arrays and pointers, passing by value and reference, Address arithmetic. Basics of Pointer to pointers.

Unit V File Handling

Modes for files, functions used in files (putchar, getchar, getc, putc, fopen, fclose, fscanf, fprint,fseek, ftell, fread and (write), error handling in files.

 

BIF 124  Networking & Internet Programming

Unit I Introduction to network

Network Goals, Kinds, HW/SW Requirements of Networking, Basic terminology associated with network, Njetwork topologies, Only a brief introduction of distributed systems, Concept of distributed Computing, Advantage & Disadvantage Internet protocol: TCP/IP, dialup access, direct access, three levels of internet connectivity, ISPs, Introduction to DNS.

Unit II Internet:

History and evolution of Internet. Internet and intranet, Basic concept of www, HTTP, FTP, URL, domain name, IP address, web browser, web server, web page, web site, portals, email, chatting, usenet, telnet, newsgroup, fax, telephony, telecommuting, conferencing, searching, downloading, uploading, files on internet, search engines. Email (reading, ending, deleting, replying), voice and video conferencing.

Unit III Internet Security & HTML

Overview of Internet security, access security, transaction security, security zones, digital IDS, sending / receiving signed and encrypted emails. Introduction to firewalls.

Unit IV Web page design through HTML

Static and dynamic web pages. Introduction to HTML, HTML elements and tags, formatting with HTML tags, physical, logical HTML styles, setting fonts, colors and headings, displaying plain, presenting and arranging text using <DIV>, <SPAN>, <LAYERS> tags. Working with images, links and lists, creating tables, working with frames, creating  horizontal, vertical frames, named frames, opening new browser window, creating HTML forms, adding controls on forms, submitting data from forms, working with multimedia, multimedia sound, video, 3D using multimedia files, inline sound and videos. Style sheets: types, creating and using style sheets.

Unit V Java Script, XML & AJS

Introduction to client and server side scripting. Introduction to Java script, data types, operators, conditional statement, loops in Java script, functions, arrays, objects and elements in Java script, Form validation using Java script. Introduction to XML, creating XML, documents, specifying attributes in DTDs, accessing XML data with XML Data Island, documents. Handling events while loading XML documents. AJS (Automated Java Script).

 

BIF 125  Biochemistry

Unit I Chemical foundations of Biology

pH, pK, acids, bases, buffers, chemical bonds, Bioenergetics: Principles of thermodynamics: free energy, important energy, rich molecules, standard free energy change, concept of redox reactions. Principles of self assembly, Hierarchy of molecular organization of living systems.

Unit II Amino acids and proteins

Classification, Chemical Reactions and Physical Properties, purification and criteria for homogeneity, structural organization of proteins- primary, secondary, tertiary and quaternary structure. Conformational analysis. Ramachandran plot.

Unit III Carbohydrates

Classification and reactions, types, structural features. Metabolism of carbohydrates, main sources of carbohydrates, enzymatic conversion and mobilization as glucoses or fructoses, glycolysis, Krebs cycle, terminal oxidation/ oxidative phosphorylation, mechanism of ATP synthesis, rate controlling steps and regulation.

Unit IV Lipids

Classification, Structure and functions, Biosynthesis of saturated and unsaturated fatty acids, Metabolism of Lipid and fat bodies: Beta-oxidation and channeling of the products to ATP production: minor pathway of fatty acid oxidation, (alpha and omega oxidation), Biosynthesis of saturated and unsaturated fatty acids, Ketone bodies, membrane lipids-cholesterol, phospholipid and glycolipid; biosynthesis of fat soluble vitamins; biosynthesis of Eicosonoids (prostaglandin, leucotriens and thromboxane).

Unit V Enzymes

Kinetics: Rate of reactions, specific activity, molecular activity, Km, Kcat, Michaelis-Menten and Line weaver Burk plot, enzyme inhibition, mechanism of enzyme catalysis (acid-base electrostatic, metal ion, free radicals, transition state binding and covalent catalysis, proximity and orientation effects, contribution of strain. Factors affecting enzyme activity, enzyme inhibition. Allosteric enzymes and bisubstrate reactions. Rationale for modification of enzyme function, Enzyme Engineering: modification of structure and catalytic properties of enzymes

Practicals

BIF 126  Bioinformatics Laboratory I

Practical based on BIF 121, 122 & 125

BIF 127 Computer Laboratory I

Practical based on BIF 123 & 124

 

Semester - II

 

BIF 221 Molecular Biology

Unit I Basics of Molecular Biology

Structure and properties of nucleic acids, Prokaryotic gene structure and organization, Eukaryotic genome structure and chromosome organization, DNA Replication in prokaryotes & eukaryotes, enzymes and accessory proteins involved in DNA Replication. Recombination (Holliday model), FLP/ FRT and Cre/ Lox recombination, Rec A and other recombinases.

Unit II Central dogma of molecular biology

Transcription in prokaryotes and eukaryotes, Transcription factors, regulation of transcription. Genetic code, Translational machinery, mechanisms of initiation, elongation and termination, regulation of translation, Co and post- translational modifications of proteins.

Unit III Gene Mutations & Chromosomal aberrations

Molecular basis of mutation, spontaneous & induced mutations, chemical and physical mutagens, Ames test. DNA repair mechanisms-photo reactivation, excision repair, mismatch repair, recombination repair, and SOS response.

Unit IV Signal transduction and cell cycle

Molecular basics of signal transduction in bacteria, plants and animals, secondary messengers, perception of environmental signals, G- protein and tyrosine kinase coupled receptors.

Cell cycle and apoptosis: Events in cell cycle, mitosis and meiosis, Key regulators of cell cycle, programmed cell death and its control. Oncogenesis

Unit V Immunology

Immunity; basic types, Cells of immune system, Antigen and it’s properties, antibodies & it’s types, effector mechanisms.

 

BIF 222  Structural Bioinformatics

Unit I Molecular Structure

Proteins: Principles of protein structure; physico-chemical properties, anatomy of proteins– Hierarchical organization of protein structure - Primary. Secondary, Supersecondary, Tertiary and quaternary structure; Molecular forces (Covalent & noncovalent); Ramachandran Map, protein folding (Chaperones and Chaperonins); DNA & RNA: structure & types of DNA double helices A,B,Z; geometrical & structural features; DNA-Protein interactions, t-RNA tertiary structure, databases of structure of protein, nucleotide & other small molecules.

Unit II Secondary & Tertiary structure Prediction

Secondary structure: Basic principles on which the prediction methods of first, second and third generation are based; algorithms of Chou Fasman, GOR methods; PHD, PSIPRED methods; concepts in measuring the accuracy of predictions (Q3, Segment overlap, Mathew’s correlation coefficient etc.); t-RNA structure prediction. Homology Modeling, Fold recognition or threading, Ab initio methods; automated methods.

Unit III Structure Comparison and Classification

Protein structure comparison and classification: classes, folds (SCOP, CATH); the concepts in 3D structure omparison, purpose of structure comparison, algorithms such as FSSP, VAST and DALI; Protein-protein interactions databases such as DIP, PPI server and tools for analysis of protein-protein interactions,

Unit IV Molecular Simulations

Molecular Mechanics Based: Introduction to Molecular and Quantum Mechanics, Concepts of force fields, Potential Energy Functions; Molecular fitting; Energy Minimisation (Non-derivative and derivative methods);Conformational searches, Geometry optimization algorithms: Steepest descents, conjugate gradient; Description of Forcefield such as MM3, Dreiding, AMBER, CHARMM etc.

Unit V Molecular Dynamics Simulations

Newton's equations for many particles, Verlet algorithms, Types of dynamics simulations: adiabatic, constant T, annealed, etc., Conformational searching using MD and other methods, Free energy calculations, Dynamics of Bio-macromolecules; Application of Molecular Simulation.

 

BIF 223  Data Structures and Algorithms

Unit I Introduction to Data Structures

Basic Data Structures: Arrays, Linked Lists, Stack, Queue, Dequeue, Tree, Heap, Hash Table and Collision resolution.

Unit II Sorting

Basic algorithms for Creation, Manipulation of Data Structures Internal Sorting Algorithms: Bubble, Heap, Quick Sort. Tape sorting and Merging

Unit III Algorithms

Simple Algorithms, Analyzing Algorithms, Asymptotic Notation. Advanced algorithim.

Unit IV Design Methods

General Consideration, Algorithm Design Paradigms and Representative Problems: Divide and Conquer (Binary search, Merge Sort), Greedy Method (Minimal Spanning Tree), Dynamic Programming (Chained Matrix Multiplication), Longest common subsequence, Backtracking (8-queens problem), Branch and Bound (0/1 Knapsack Problem) String Matching Problem, Brute Force Method, KMP Algorithm, Boyer- Moore Algorithm, Approximate String matching.

Unit V Intractable Problems

Basic Concepts, Nondeterministic Algorithms, NP Completeness (Brief introduction only- no proof) , optimization algorithim.

 

BIF 224  Object Oriented Programming Languages

Unit – I

Introduction to OO Paradigm,Structured Versus object oriented programming,Objects and Class,features of object oriented language(encapsulation,data abstraction,inheritance, Object  composition, Polymorphism) Merits & demerits of OO methodology, Hello World Program and C++ program structure

Unit-II

Data Types,Operators: keywords, data types and size, Variables, constants, Operators(Arithmetic, Relational ,logical, Compound assignment, Increment ,decrement and conditional operator ) .

Expression and Precedence : Arithmetic, Relational ,logical Expression ,Operator Precedence and associatively, promotion and type casting , Different types of comments

Unit-III

Control Flow : Statement and blocks , if statement . if –else statement, Nested if –else statement , Switch statement , Break , continue statement , While , for and do-while loops Scope and Visibility control Modifier

Arrays and Functions: Arrays , operations on Arrays , Multi-Dimensional Arrays ,Strings ,Strings manipulations and Arrays of strings, functions , Parameter passing ,Return by reference, inline functions ,Arrays and functions. Library functions. Virtual Functions, Exception Handling, I/O Streams File handling in C++.

Unit-IV

Introduction to Core Java

Java Basics, Java Programming Tools, Creating Classes and Objects in Java, Arrays, Conditionals and Loops, Applets Basics, Graphics, Fonts and Color, Simple Animation, Managing Simple Events and Interactivity, Creating User Interfaces with AWT.

Unit-V

Advance Java

Exception, Multithreading, Packages and Interfaces, Windows, Networking and other Tidbits, Access Modifiers, I/O Streams, Using Native Methods and Libraries, Working with Data Structures and Java, Image Filters.

 

BIF 225  Database Management Systems

Unit I Basic Concept

An Introduction to database System, Basic Data System Terminology, Purpose of DBMS, Data Independence, An Architecture of DBMS: Schema, Subschema, mapping,  Physical & Logical Data, Basic File Systems, File Organization: Sequential, Index Sequential, Hosting, B-Tree based index, File Organisation based on Dynamic Hashing with immediate splitting, Model of Real World, Details of E-R Model.

Unit II Three Data Models

An Overview of three Main Data Models i.e. Hierarchical Model, Network Model, Relational Model and their Inter comparison, Concept of Relation, Relational Algebra: Basic Operation like Union, Intersection, Difference, Product Join, The relational Calculus: Domain & Tuple Calculus, Relational Database Design: Integrity Constraints, Functional Dependency: Single Value and Multi Value Functional dependency, Normal Forms: I, II, III, Boycee Codd, & IVth Normal forms; Join Dependency.

Unit III Query Processing & Database Software

Query Interpretation, Equivalence of Expression, Estimation of Query Processing Cost, Query Optimization by Algebraic Manipulation, Join Algorithms, Types of Data Base Languages: Procedural and Non-procedural Language, Relational Commercial Query languages,QBE,

Unit IV SQL implementation

SQL: Introduction, Basic Structure, the Power of SQL (Creation, Insertion, Deletion, Indexing & Modification of Databases in SQL), query optimization strategies.

Unit V Management Considerations & Future Trends: Security & Integrity

Introduction, Access Control, Crypto Systems, Statistical DataBase Security; Concurrency Control: Transaction, Database System Architecture, Serializability, Locking, Database Recovery: Kinds of Failure, Recovery Techniques, Object, An Overview of Oriented Model, Distributed database: Structure, Tradeoffs, Design, Client Server Database, Knowledge databases.

Practicals

BIF 226 & BIF 227 Computer Laboratory II (Based on BIF 123 & 124)

Practical based on

• Arrays
• Linked lists
• Stack
• Queue
• Dequeue
• Tree

 

Semester - III

BIF 321  Bioinformatics Algorithms and Perl Programming

Unit I Sequence Alignment and Comparison Methods

Alignment Basics, Local and Global Alignment, DOT Matrix Analysis, Scoring System, Evolutionary Matrices (PAM, BLOSUM), PSSM, Dynamic Programming: Smith-Waterman and Needleman-Wunsch Algorithms, BLAST & FASTA Algorithms, Statistical Significance, PSI & PHI Blast.

Unit II Multiple Sequence Alignment

MSA Basics, MSA Scoring: Entropy & Sum of Pairs Method, Multi dimensional Dynamic Programming and Progressive Alignment Method, ClustalW/X tool.

Unit III Phylogenetics Analysis

The phylogeny problem, Tree Basics & Topology, Ultrametric property, Tree Reconstruction Methods (UPGMA, NJ, Parsimony & Maximum Likelihood), Boostrapping,

Unit IV Bioinformatics Programming in PERL

Perl variables and Data types (Scalar, List, Array and Hash), Default variables, Conditional Expressions, Iterations, Subroutines, File handling, Regular expressions, References, Anonymous data types, Perl-CGI, Perl Modules and Packages, basic arithmetic calculation, string function, mathematical and time function

Unit V Bio perl

OOPs Concept, BioPerl Module, Object & Classes, Implementing Bioperl Modules, CPAN Library.

 

BIF 322  Essentials of Statistics

Unit I Statistical Measurements

Classification & Tabulation of Data, Central tendency (Mean, Median, Mode), Dispersion (Absolute and Relative variation, Range, Deviationsquartiles and percentile), Variance, Covariance, RMSD.

Unit II Probability distribution

Terms and concepts, Definition, Simple problems involving probability, Conditional Probability Distribution Functions (Discrete and Continuous R.V.), Normal, Binomial, Poisson, Central Limit Theorem

Unit III Multivariate Statistics

ANOVA, Correlation, Covariance, Calculation of covariance, Correlation analysis, Types of correlation, Scatter Diagram, Regression analysis, Regression coefficients

Unit IV Statistical Inference

Test of Hypothesis, Test of Significance, types of sampling, Sampling Distribution (Chi- Square, Students t and F test)

Unit V Statistical Bioinformatics

Markowian process. Markow & hidden Markow model & it’s applications to bioinformatics. Stochastic process.

 

BIF 323  Biophysical Techniques

Unit I Spectroscopy

Interaction of light and matter, absorption spectroscopies (UV/vis and infrared), Fluorescence, and Circular Dichroism, Protein IR and FTIR spectroscopy

Unit II Chromatography & Electrophoresis

Column Chromatography, Paper Chromatography, Thin layer Chromatography; Liquid chromatography (Ion exchange, gel permeation and affinity chromatography);Gas Chromatography

Electrophoresis: Isoelectric Focussing, Gel Electrophoresis, 2D electrophoresis, Protein detection, 2D DIGE, Proteomic Databases & tool.

Unit III X-Ray Crystallography

Properties of crystals and foundations of X-ray diffraction; the phase problem and  methods for its solution including isomorphous replacement, molecular replacement, and multiwavelength anomalous dispersion; model building and model refinement; model analysis.

Unit IV NMR Spectroscopy

Principles of nuclear magnetic resonance (NMR), multidimensional NMR spectroscopy, including COSY, TOCSY and NOESY experiments, sequential assignments and structural analysis, practical methods and new developments in the field.

Unit V Mass Spectrometry Based Proteomics

Basics, Spectra, Sample Preparation, Mass Spectrometry Ionization Techniques, Mass analyzers,Peptide fragmentation mechanism, Interpretation of Mass Spectra. Various techniques: Ion-trap (Linear & Quadrupole), MALDI-TOF, LC-ESI-TOF, and LC-ESIMS/MS

 

BIF 324  Molecular Genetics & Genomics

Unit I Genome Basics

Chromosomes structure and Genome Organization. Structure of Prokaryotic & Eukaryotic Genes, Transposable Genetics Elements, Repetitive elements, LINE and SINES, VNTRs, Central Dogma of Molecular Biology

Unit II DNA technology

Cloning strategy, Genetic and physical mapping, molecular markers, PCR Primer & Oligos Designiing,

Unit III Genomics

Human Genome Project, Current techniques: Sanger’s method & Maxam- Gilbert method. Next Generation Sequencing Techniques, Sequence Assembly and Annotation, ORFs, Gene Identification and Prediction Methods, Genome Alignment and Comparative Genomics. Pyrosequencing & its modifications: Solexa, 454 sequencing.

Unit IV Microarray

Microarray Basics, DNA Hybridization, DNA & Protein chips. Experimental Design: Features, target Preparation, Labeling & Sensitivity, Spotting media.

Microarray Data analysis: image and raw data, Preprocessing & Normalization methods, Pattern Finding & Clustering. Statistical Tests and differential gene expression analysis, Applications of Microarray Technology.

Unit V Microarray Databases and Tools

GEO, YMD, SMD, ArrayExpress etc. SNOMAD, magic tool(open software). Bioconductor, Commercial & Open Source tools for microarray.

 

 

BIF 325 A  Computer Aided Drug Designing

Unit I Introduction to Drug discovery life cycle

Lead to Drug, Classical steps, Chemical Parameters in drug design, Drug Control Authorities (CDA/CDSCO, FDA), Clinical Trials, GCP guidelines, Schedule Y.

Unit II Chemoinformatics I

Introduction, History, Current activities and Challenges Chemical Databases and libraries, Chemical File formats and LIMS Database, Representation of Structures: 2D & 3D, Structural drawing and visualization tools.

Unit III Chemoinformatics II

Molecular Descriptors, Pharmacophore Identifications, Drug Potency and Efficacy. Pharmacodynamics, Pharmacokinetics and Toxicology of compounds, ADME/T Analysis, Quantitative Structure Activity Relationships (QSAR) and its applications

Unit IV Molecular Docking

Molecular Surface & Accessible Surface Area, Rigid body & Flexible docking, Proteinprotein and Protein-Ligand Docking, Scoring Methods, Conformational Searching and Scoring, Application of Molecular Docking, Molecular Docking tools (Dock & Autodock, Hex, Arguslab etc).

Unit V Drug designing

Drug Target Identification, Virtual Screening of Compounds. CADD: Structure based and Analog based drug designing (Ligand, Receptor and Pharmacophore Based Approaches).

 

 

BIF 325 B  Machine Learning & Soft Computing Techniques

Unit I Machine Learning Foundations & Algorithms

The Probabilistic Framework Bayesian Modeling, The Cox-Jaynes Axioms, Probabilistic Modeling and Inference Dynamic Programming, Gradient Descent, EM/GEM Algorithms, Markov Chain Monte Carlo Methods, Simulated Annealing, Evolutionary and Genetic Algorithms, Learning Algorithms

Unit II Neural Networks

Theory- Introduction, Universal Approximation Properties, Priors and Likelihoods, Learning Algorithms: Back propagation, Application in Bioinformatics, SNNS tool.

Unit III Hidden Markov Models & hybrid system

Introduction, Prior Information and Initialization, Likelihood and Basic Algorithms, Learning Algorithms, Advantages and Limitations of HMMs. Applications in Bioinformatics, HMMer tool.

Hybrid Systems: HMM & Neural Networks - Introduction to Hybrid Models, The Single- Model Case, The Multiple-Model Case, Simulation Results

Unit IV Genetic Algorithm & Fuzzy methods

Genetic Operators and Parameters, Theoretical Foundations of Genetic Algorithms, Implementation issues, Application in Bioinformatics

Introduction to Fuzzy Sets, Operations on Fuzzy sets, Fuzzy Relations, Fuzzy Measures, Applications in Bioinformatics

Unit V Support Vector Machines

The Learning Methodology, Linear Methods, Kernels, Feature Spaces, Generalization & Optimization Theory, Implementation, Applications in Bioinformatics, SVM lite tool.

 

BIF 325 C  Computer Graphics

Unit I

Overview: Graphical system, Different types of display devices,

Unit II

Software: GUI concepts, PHIGS, GKS.

Design concepts: point, and line drawing, curve generation

Unit III.

Concepts of 2D graphics: translation, rotation, scaling, clipping.

Unit IV

3D graphics: Modelling, Transformation and viewing, Color models

Unit V

Principles of animation

Open GL application for windows programming

 

 

BIF 325 D  Genomics and Proteomics

Unit I: Genomics

Chromosome structure and Genome organization, Genome sequencing methods, Genome assembly, gene identification methods, Genome annotation techniques, Comparative genomics.

Unit II: Genetic and physical mapping:

Introduction to molecular markers-RFLP, RAPD, AFLP, SSRs and others. Genetic and physical maps, map based cloning, mapping population, southern and in situ hybridization for genome analysis. Single nucleotide polymorphisms, Genome evolution, DNA microarrays, Genomics in drug discovery.

Unit III: Proteomics

• Proteomics Basics and 2D Gel Electrophoresis.
• Protein Identification and Analysis.
• Protein preparation and Seperation.
• Protein Identification by mass spectrometry.
• Identification of post translation modification.

Unit IV: Protein Mapping

Protein Expression Mapping, High –throughput cloning of ORFs, Protein –Protein Interaction Mapping: Experimental and Computational

Unit V: Microarray

Microarray-the technique, Experimental design and Data analysis, Application of Microarray, Proteins Arrays and Protein Chips, Proteomics Tools and Databases.

 

Practicals

BIF 326  Practical paper Bioinformatics lab III (Based on BIF 321)

BIF 327  Practical paper  Computer lab III  Based on BIF 324 and 325 (A-D) )

 

Semester – IV

Project Work